source: cpp/frams/genetics/f4/f4_general.h @ 829

Last change on this file since 829 was 829, checked in by Maciej Komosinski, 7 months ago

Removed unnecessary cast, "long" is equivalent to "int" in our compilations

  • Property svn:eol-style set to native
File size: 18.3 KB
Line 
1// This file is a part of Framsticks SDK.  http://www.framsticks.com/
2// Copyright (C) 1999-2015  Maciej Komosinski and Szymon Ulatowski.
3// See LICENSE.txt for details.
4
5// Copyright (C) 1999,2000  Adam Rotaru-Varga (adam_rotaru@yahoo.com), GNU LGPL
6
7#ifndef _F4_GENERAL_H_
8#define _F4_GENERAL_H_
9
10#include <frams/util/3d.h>
11#include <frams/util/sstring.h>
12#include <frams/util/multirange.h>
13#include <frams/genetics/geneprops.h>
14
15#ifdef DMALLOC
16#include <dmalloc.h>
17#endif
18
19/**
20 * Performs single rotation angle decrementation on a given value.
21 * @param v pointer to the decremented value
22 */
23void rolling_dec(double *v);
24
25/**
26 * Performs single rotation angle incrementation on a given value.
27 * @param v pointer to the incremented value
28 */
29void rolling_inc(double *v);
30
31class f4_node;   // later
32class f4_Cell;   // later
33class f4_Cells;  // later
34
35
36/** @name Types of f4_Cell's */
37//@{
38#define T_UNDIFF4 40 ///<undifferentiated cell
39#define T_STICK4  41 ///<differentiated to stick, cannot divide
40#define T_NEURON4 42 ///<differentiated to neuron, can divide
41//@}
42
43/**
44 * Scans f4 genotype string for a stopping character and returns the position of
45 * this stopping character or 1 if the end of string was reached. This method is used
46 * for closing braces, like ), >, ]. It runs recursively when opening braces
47 * like (, <, # are found.
48 * @param s string with the f4 genotype
49 * @param slen length of a given string
50 * @param stopchar character to be found
51 * @return 1 if end of string was reached, or position of found character in sequence
52 */
53int scanrec(const char* s, unsigned int slen, char stopchar);
54
55
56class f4_CellLink;
57
58/** @name Constraints of f4 genotype structures */
59//@{
60#define MAXINPUTS 100 ///<maximum number of neuron inputs
61#define MAX4CELLS 100 ///<maximum number of f4 organism cells
62//@}
63
64/**
65 * Abstract cell type - the representation of single component in the  developmental
66 * encoding. In the beginning, each f4_Cell is undifferentiated. During the process
67 * of development it can divide or differentiate into a stick or a neuron. If it
68 * differentiates to a neuron, then it preserves the ability to divide, but divided
69 * cells will be the same type as the parent cell. If it is a stick, then it cannot
70 * be divided anymore.
71 *
72 * From f4_Cell array the final Model of a creature is created.
73 */
74class f4_Cell
75{
76public:
77        /**
78         * Represents the repetition marker. It holds information about the pointer
79         * to the repetition node and the count of repetitions.
80         */
81        class repeat_ptr
82        {
83        public:
84                repeat_ptr() : node(NULL), count(-1) { };
85
86                /**
87                 * A constructor that takes the pointer to the repetition node and the count of repetitions.
88                 * @param a pointer to f4_node for repetition character
89                 * @param b the number of repetitions
90                 */
91                repeat_ptr(f4_node *a, int b) : node(a), count(b) { };
92
93                inline void makeNull() { node = NULL; count = -1; };
94
95                inline bool isNull() const { return ((node == NULL) || (count <= 0)); };
96
97                inline void dec() { count--; };
98                f4_node    *node; ///<pointer to the repetition code
99                int       count; ///<repetition counter
100        };
101
102        /**
103         * Represents the stack of repeat_ptr objects. The objects are
104         * pushed to the stack when '#' repetition symbol appears, and are popped when
105         * the end of the current cell definition, i.e. the '>' character, appears. After the
106         * '>' character, the cell is duplicated as many times as it is defined after the
107         * repetition marker.
108         */
109        class repeat_stack
110        {
111        public:
112                repeat_stack() { top = 0; }
113
114                inline void clear() { top = 0; }
115
116                /**
117                 * Pushes repeat_ptr object onto the stack. If the stack size is exceeded, then no
118                 * information is provided.
119                 * @param rn repetition node info
120                 */
121                inline void push(repeat_ptr rn) { if (top >= stackSize) return; ptr[top] = rn; top++; }
122
123                inline void pop() { if (top > 0) top--; }
124
125                /**
126                 * Gets the current top element.
127                 * @return pointer to the element on top of the repeat_stack object
128                 */
129                inline repeat_ptr* first() { return &(ptr[top - (top > 0)]); };
130                static const int stackSize = 4;  ///<max 4 nested levels
131                repeat_ptr ptr[stackSize]; ///<array holding pointers to repeat_ptr
132                short int top;  ///<index of the top of the stack
133        };
134
135        /**
136         * Creates a new f4_Cell object.
137         * @param nname name of a cell, can be T_UNDIFF4, T_STICK4 or T_NEURON4
138         * @param ndad pointer to the parent of the created cell
139         * @param nangle the amount of commas affecting branch angles
140         * @param newP genotype properties of a given cell
141         */
142        f4_Cell(int nname, f4_Cell *ndad, int nangle, GeneProps newP);
143        /**
144         * Creates a new f4_Cell object.
145         * @param nO pointer to an organism containing the cell
146         * @param nname name of the cell, can be T_UNDIFF4, T_STICK4 or T_NEURON4
147         * @param ngeno pointer to the root of the genotype tree
148         * @param ngcur pointer to the f4_node representing the current cell in the genotype tree
149         * @param ndad pointer to the parent of the created cell
150         * @param nangle the number of commas affecting branch angles
151         * @param newP genotype properties of a given cell
152         */
153        f4_Cell(f4_Cells *nO, int nname, f4_node *ngeno, f4_node *ngcur, f4_Cell *ndad, int nangle, GeneProps newP);
154
155        ~f4_Cell();
156
157        /**
158         * Performs a single step of cell development. This method requires a pointer to
159         * the f4_Cells object in org attribute. If the current node in genotype tree
160         * is the branching character '<', the cell divides into two cells, unless the
161         * cell was already differentiated into the stick cell. Otherwise, the current
162         * differentiation or modification is performed on the cell. If current node is
163         * creating a connection between two neuron nodes and the input node is not
164         * yet developed, the simulation of the development of the current cell waits until
165         * the input node is created. The onestep method is deployed for every cell
166         * at least once. If one cell requires another one to develop, onestep
167         * should be deployed again on this cell. This method, unlike genotype tree
168         * creation, checks semantics. This means that this function will fail if:
169         *  - the cell differentiated as a stick will have branching node '<',
170         *  - the undifferentiated cell will have termination node '>' (end of cell development without differentiation),
171         *  - the stack of repetition marker '#' will exceed maximum allowed value of repetition,
172         *  - the stick modifiers, like rotation, will be applied on neuron cell,
173         *  - the differentiated cell will be differentiated again,
174         *  - the neuron class inside cell connection (i.e. N[G:5]) is not a sensor,
175         *  - the connection between neurons cannot be established,
176         *  - the neuron class is not valid.
177         *
178         * @return 0 if development was successful, 1 if there was an error in genotype tree
179         */
180        int onestep();
181
182        /**
183         * Adds a link between this neuron cell and a given neuron cell in nfrom. If the nfrom object
184         * is not given, neuron type in nt should be a sensor type.
185         * @param nfrom input neuron cell, or NULL if not given
186         * @param nw weight of connection
187         * @param nt empty string or name of sensor class
188         * @return 0 if link is established, -1 otherwise
189         */
190        int   addlink(f4_Cell *nfrom, double nw, string nt);
191
192        /**
193         * Adjusts properties of stick objects.
194         */
195        void  adjustRec();
196
197        int        name;               ///<name of cell (number)
198        int        type;               ///<type
199        f4_Cell *dadlink;              ///<pointer to cell parent
200        f4_Cells  *org;                ///<uplink to organism
201
202        f4_node *genot;                    ///<genotype tree
203        f4_node *gcur;                 ///<current genotype execution pointer
204        int active;                    ///<determines whether development is still active
205        repeat_stack repeat;           ///<stack holding repetition nodes and counters
206        int recProcessedFlag;          ///<used during recursive traverse
207        MultiRange genoRange;          ///<remember the genotype codes affecting this cell so far
208
209        GeneProps    P;                ///<properties
210        int          anglepos;         ///<number of position within dad's children (,)
211        int          childcount;       ///<number of children
212        int          commacount;       ///<number of postitions at lastend (>=childcount)
213        double       rolling;          ///<rolling angle ('R') (around x)
214        double       xrot;                         ///<rotation angle around x
215        double       zrot;             ///<horizontal rotation angle due to branching (around z)
216
217        double       mz;               ///<freedom in z
218        int          p2_refno;         ///<the number of the last end part object, used in f0
219        int          joint_refno;      ///<the number of the joint object, used in f0
220        int          neuro_refno;      ///<the number of the neuro object, used in f0
221
222        int          ctrl;             ///<neuron type
223        double       inertia;          ///<inertia of neuron
224        double       force;            ///<force of neuron
225        double       sigmo;            ///<sigmoid of neuron
226        f4_CellLink *links[MAXINPUTS]; ///<array of neuron links
227        int          nolink;           ///<number of links
228        NeuroClass *neuclass;          ///<pointer to neuron class
229};
230
231/**
232 * Class representing link between neuron cells.
233 */
234class f4_CellLink
235{
236public:
237        /**
238         * Constructor for f4_CellLink class. Parameter nfrom represents input
239         * neuron cell or NULL if connection has defined sensor type inside, like "[G:5]".
240         * The name of sensor class defined inside neuron connection is stored in the nt
241         * parameter.
242         * @param nfrom pointer to input neuron cell or NULL
243         * @param nw weight of connection
244         * @param nt name of neuron class or empty string
245         */
246        f4_CellLink(f4_Cell *nfrom, double nw, string nt);
247
248        f4_Cell *from; ///<pointer to input neuron cell
249        string t;      ///<empty if 'from' cell is given, NeuroClass name otherwise
250        double w;      ///<weight of connection
251};
252
253
254/**
255 * A class representing a collection of cells. It is equivalent to an organism.
256 */
257class f4_Cells
258{
259public:
260
261        /**
262         * Constructor taking genotype in a form of a tree.
263         * @param genome genotype tree
264         * @param nrepair 0 if nothing to repair
265         */
266        f4_Cells(f4_node *genome, int nrepair);
267
268        /**
269         * Constructor taking genotype in a form of a string.
270         * @param genome genotype string
271         * @param nrepair 0 if nothing to repair
272         */
273        f4_Cells(SString &genome, int nrepair);
274
275        /**
276         * Destructor removing cells from memory.
277         */
278        ~f4_Cells();
279
280        /**
281         * Adds a new cell to organism.
282         * @param newcell cell to be added
283         */
284        void addCell(f4_Cell *newcell);
285
286        /**
287         * Creates an approximate genotype in the f1 encoding and stores it in a given parameter.
288         * @param out the string in which the approximate f1 genotype will be stored
289         */
290        void toF1Geno(SString &out);
291
292        /**
293         * Performs a single step of organism development. It runs each active cell
294         * in the organism.
295         * @return 0 if all cells are developed, or 1 otherwise
296         */
297        int  onestep();
298
299        /**
300         * Performs the full development of organism and returns error code if something
301         * went wrong.
302         * @return 0 if organism developed successfully, error code if something went wrong
303         */
304        int  simulate();
305
306        /**
307         * Returns error code of the last simulation.
308         * @return error code
309         */
310        int  geterror() { return error; };
311
312        /**
313         * Returns position of an error in genotype.
314         * @return position of an error
315         */
316        int  geterrorpos() { return errorpos; };
317
318        /**
319         * Sets error code GENOPER_OPFAIL for a simulation on a given position.
320         * @param nerrpos position of an error
321         */
322        void setError(int nerrpos);
323
324        /**
325         * Sets the element of genotype to be repaired by removal.
326         * @param nerrpos position of an error in genotype
327         * @param rem the f4_node to be removed from the  genotype tree in order to repair
328         */
329        void setRepairRemove(int nerrpos, f4_node *rem);
330
331        /**
332         * Sets repairing of a genotype by inserting a new node to the current genotype.
333         * @param nerrpos position of an error in genotype
334         * @param parent the parent of a new element
335         * @param insert the element to be inserted
336         * @return 0 if repair can be performed, or -1 otherwise because the repair flag wasn't set in the constructor
337         */
338        int  setRepairInsert(int nerrpos, f4_node *parent, f4_node *insert);
339
340        /**
341         * Repairs the genotype according to setRepairRemove or setRepairInsert methods.
342         * @param geno pointer to the genotype tree
343         * @param whichchild 1 if first child, 2 otherwise
344         */
345        void repairGeno(f4_node *geno, int whichchild);
346
347        // the cells
348        f4_Cell *C[MAX4CELLS];  ///<Array of all cells of an organism
349        int       nc;           ///<Number of cells in an organism
350
351private:
352        // for error reporting / genotype fixing
353        int repair;
354        int error;
355        int errorpos;
356        f4_node *repair_remove;
357        f4_node *repair_parent;
358        f4_node *repair_insert;
359        void toF1GenoRec(int curc, SString &out);
360        f4_Cell *tmpcel;                // needed by toF1Geno
361        f4_node *f4rootnode;          // used by constructor
362};
363
364
365/**
366 * A class to organize a f4 genotype in a tree structure.
367 */
368class f4_node
369{
370public:
371        string name; ///<one-letter 'name', multiple characters for classes
372        f4_node *parent; ///<parent link or NULL
373        f4_node *child; ///<child or NULL
374        f4_node *child2; ///<second child or NULL
375        int pos; ///<original position in the string
376        int i1; ///<internal int parameter1
377        int l1; ///<internal long parameter1 (now also int, since long is not well specified and it is in our scenarios equivalent to int)
378        double f1; ///<internal double parameter1
379        string s1; ///<internal string parameter1
380
381        f4_node();
382
383        /**
384         * Multiple-character name constructor.
385         * @param nname string from genotype representing node
386         * @param nparent pointer to parent of the node
387         * @param npos position of node substring in the genotype string
388         */
389        f4_node(string nname, f4_node *nparent, int npos);
390
391        /**
392         * Single-character name constructor.
393         * @param nname character from genotype representing node
394         * @param nparent pointer to parent of the node
395         * @param npos position of node character in the genotype string
396         */
397        f4_node(char nname, f4_node *nparent, int npos);
398
399        ~f4_node();
400
401        /**
402         * Adds the child to the node.
403         * @param nchi the child to be added to the node
404         * @return 0 if the child could be added, -1 otherwise
405         */
406        int addChild(f4_node *nchi);
407
408        /**
409         * Removes the child from the node.
410         * @param nchi the child to be removed from the node
411         * @return 0 if child could be removed, -1 otherwise
412         */
413        int removeChild(f4_node *nchi);
414
415        /**
416         * Returns the number of children.
417         * @return 0, 1 or 2
418         */
419        int childCount();
420
421        /**
422         * Returns the number of nodes coming from this node in a recursive way.
423         * @return the number of nodes from this node
424         */
425        int count();
426
427        /**
428         * Returns the nth subnode (0-)
429         * @param n index of the child to be found
430         * @return pointer to the nth subnode or NULL if not found
431         */
432        f4_node* ordNode(int n);
433
434        /**
435         * Returns a random subnode.
436         * @return random subnode
437         */
438        f4_node* randomNode();
439
440        /**
441         * Returns a random subnode with a given size.
442         * @param min minimum size
443         * @param max maximum size
444         * @return a random subnode with a given size or NULL
445         */
446        f4_node* randomNodeWithSize(int min, int max);
447
448        /**
449         * Prints recursively the tree from a given node.
450         * @param buf variable to store printing result
451         */
452        void      sprintAdj(char *&buf);
453
454        /**
455         * Recursively copies the genotype tree from this node.
456         * @return pointer to a tree copy
457         */
458        f4_node* duplicate();
459
460        /**
461         * Recursively releases memory from all node children.
462         */
463        void      destroy();
464private:
465        void     sprint(SString &out);  // print recursively
466};
467
468/**
469 * The main function for converting a string of f4 encoding to a tree structure. Prepares
470 * f4_node root of tree and runs f4_processrec function for it.
471 * @param geno the string representing an f4 genotype
472 * @return a pointer to the f4_node object representing the f4 tree root
473 */
474f4_node* f4_processtree(const char *geno);
475
476/**
477 * Scans a genotype string starting from a given position. This recursive method creates
478 * a tree of f4_node objects. This method extracts each potentially functional element
479 * of a genotype string to a separate f4_nodes. When the branching character '<' occurs,
480 * f4_processrec is deployed for the latest f4_node element. This method does not
481 * analyse the genotype semantically, it only checks if the syntax is proper. The only
482 * semantic aspect is neuron class name extraction, where the GenoOperators
483 * class is used to parse the potential neuron class name.
484 * @param genot the string holding all the genotype
485 * @param pos0 the current position of processing in string
486 * @param parent current parent of the analysed branch of the genotype
487 * @return 0 if processing was successful, otherwise returns the position of an error in the genotype
488 */
489int f4_processrec(const char *genot, unsigned pos0, f4_node *parent);
490
491/**
492 * Parses notation of the neuron connection - takes the beginning of the connection
493 * definition, extracts the relative position of input neurons and the weight of the connection.
494 * After successful parsing, returns the pointer to the first character after the connection
495 * definition, or NULL if the connection definition was not valid due to the lack of [, :, ]
496 * characters or an invalid value of relfrom or weight.
497 * @param fragm the beginning of connection definition, should be the '[' character
498 * @param relfrom the reference to an int variable in which the relative position of the input neuron will be stored
499 * @param weight the reference to a double variable in which the weight of the connection will be stored
500 * @return the pointer to the first character in string after connection definition
501 */
502const char *parseConnection(const char *fragm, int &relfrom, double &weight);
503
504/**
505 * Parses the notation of the neuron connection with neuron definition - takes
506 * the beginning of the connection definition, extracts the name of neuron class
507 * that will be the input for the current neuron and the weight of the connection.
508 * After successful parsing, returns a pointer to the first character after the connection
509 * definition, or NULL if the connection definition was not valid due to the lack of [, :, ]
510 * characters, an invalid value of the weight or an invalid neuron class name.
511 * @param fragm the beginning of the connection definition, should be the '[' character
512 * @param neutype the reference to a string representing the input neuron class name. The name of the class is validated with GenoOperators::parseNeuroClass()
513 * @param weight the reference to a double variable in which the weight of the connection will be stored
514 * @return the pointer to the first character in string after the connection definition
515 */
516const char *parseConnectionWithNeuron(const char *fragm, string &neutype, double &weight);
517
518#endif
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